Hi Faith
Traffic through the Bosphorus generally moves in convoy, northbound in the morning, southbound in the afternoon, which is generally helpful for ship photography. The switch is usually around 1/2 pm but can be earlier or later. Naval vessels and cruise ships are not subject to the convoy system.
There are plenty of vantage points but the cityscape background can be a problem. Clearest spot for morning photography is a promenade near the Kadikoy ferry stop on the Asian side but a long lens is essential. Northbound ships come closest at Kandilli, the narrowest point in the straits. here you can take shots from the crumbling promenade or from the road above (which helps with background and avoids the risk of fishing rods getting in the way).
A "tourist" ferry leaves Eminonu 2/3 times each day, first one at 10.35, calling at several locations en route to Anadolu Kavagi at the northern end of the straits. Penultimate stop is Rumeli Kavagi, on the European side, which is excellent for afternoon shots (best position is from the hill about 600 metres to the south of the ferry stop and after around 2.30 when the summer has moved around).
There are several other good points for afternoon photography: the Sarayburnu tea gardens (in Gulhane park and near Topkapi palace) is sufficiently high up to avoid background clutter); Rumeli Hisari, near the 2nd Bosphorus bridge (and almost opposite Kandilli); and Tarabya, about the only point where you can take southbound traffic around midday with the sun behind you.
please send me a pm with your e-mail if you would like a map with the locations marked.
Hope you manage to get there - it's a fantastic city, not just for the ships
regards
Simon